Analyzing Contentious Relationships and Outlier Genes in Phylogenomics

Area of Science:

• Phylogenomics
• Molecular Evolution
• Bioinformatics

Background:

• Gene tree conflict is prevalent in phylogenomic analyses.
• A small fraction of genes can disproportionately influence species tree inference in supermatrix methods.
• Discrepancies between supermatrix and coalescent-based species trees are common.

Purpose of the Study:

• To investigate conflicting results between supermatrix and coalescent species tree methods.
• To identify and characterize influential outlier genes driving topological discordance.
• To evaluate a novel framework for examining phylogenetic signal in large datasets.

Main Methods:

• Analysis of two datasets with conflicting supermatrix and coalescent species trees.
• Identification and removal of highly influential outlier genes.
• Application of a new framework for edge-based phylogenetic analysis in large datasets.

Main Results:

• Removal of identified outlier genes resolved topological conflicts, aligning supermatrix trees with coalescent-based results.
• Outlier genes in a vertebrate dataset stemmed from orthology detection errors.
• Outlier genes in a plant dataset showed no obvious systematic error, suggesting potential novel biological processes.

Conclusions:

• Outlier genes can significantly mislead phylogenomic inference; their identification is critical.
• The developed framework facilitates targeted examination of phylogenetic signal without assuming a single gene topology.
• This approach enhances the understanding of underlying evolutionary signals in complex phylogenomic datasets.